Athurva Gore/LabNotes/2009-9-9

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Revision as of 22:20, 9 September 2009 by >Ajgore (→‎Exome Resequencing)
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Exome Resequencing

PGP4, 6, and 10

  • Wanted to see if using a 5 bp throwout range works well with these libraries

IPS and Cancer

LOH Mutations

  • Need to check LOH mutations; is the new variant the damaging one? Or the old one?
    • If nondamaging version is lost, this is not actually harmful to the cell...
    • Modified SIFT input to have fibroblast first, IPS second
    • Can now easily check if damage is gained or lost.
  • ALL DAMAGING MUTATIONS: The non-damaging variant was lost via LOH!
    • True for most (all but 3) tolerated mutations as well
    • Strange. Will need to investigate with Primers...

PCR Primers for target Genes

  • Need to use Primer3 to obtain PCR primers for regions of interest.
    • Have five regions of interest: 2 from GOH, 3 from LOH
    • Get book on DNA methods? Or talk to Alice or Ida about it
    • Pull out sequences of an optimal length around SNP plus flanking regions